Contacts of the helix formed by residues 213 - 225 (chain A) in PDB entry 1M9H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ALA* 3.4 5.3 - - - +
212A LYS* 1.3 79.1 - - - +
214A PRO* 1.3 77.1 - - + +
215A ALA* 3.6 2.8 + - - -
216A GLN* 3.1 27.1 + - - +
217A ALA 2.9 18.2 + - - -
241A GLU* 2.8 37.2 + - + +
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A PHE* 3.8 37.9 - - + +
203A VAL* 3.6 25.4 - - + +
204A THR* 4.8 7.6 - - + -
207A ALA* 3.9 13.0 - - + -
212A LYS 4.4 0.4 - - - +
213A THR* 1.3 90.0 - - + +
215A ALA* 1.3 63.1 + - - +
217A ALA* 2.9 3.6 + - - +
218A VAL* 2.8 26.5 + - - +
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Residues in contact with ALA 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.8 6.4 - - + +
198A PHE* 3.6 26.8 - - + -
213A THR* 3.3 7.1 + - - +
214A PRO* 1.3 76.9 - - - +
216A GLN* 1.3 58.1 + - - +
218A VAL* 3.2 3.1 + - - +
219A LEU* 2.9 35.6 + - - +
241A GLU* 4.0 0.7 - - - +
242A ASN* 4.3 3.6 - - - +
300A NAD 3.4 38.8 - - + +
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 3.3 20.3 - - + +
213A THR* 3.1 33.7 + - - +
214A PRO 3.1 0.6 - - - -
215A ALA* 1.3 81.8 - - + +
217A ALA* 1.3 57.5 + - - +
219A LEU* 3.3 4.7 + - - +
220A ARG* 2.9 29.1 + - - +
241A GLU* 2.6 53.4 + - + +
242A ASN* 5.0 1.6 - - - -
244A ASP* 3.4 25.3 + - - +
245A VAL* 3.8 17.8 - - + +
248A PHE* 3.6 6.8 - - + -
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A VAL* 4.0 10.3 - - + +
206A ALA* 4.2 11.0 - - + -
207A ALA* 3.8 28.5 - - + +
212A LYS* 4.9 0.2 - - - +
213A THR 2.9 12.1 + - - +
214A PRO 2.9 8.3 + - - +
216A GLN* 1.3 76.4 - - - +
218A VAL* 1.3 62.4 + - - +
220A ARG* 3.3 8.1 + - - +
221A TRP* 3.1 19.8 + - - +
248A PHE* 4.5 8.7 - - + -
250A LEU* 3.6 9.4 - - + +
258A ILE* 4.6 3.6 - - + +
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PRO* 4.2 10.5 - - + -
189A PRO 3.5 24.7 - - - +
190A LEU* 3.7 13.5 - - + -
197A LEU* 4.0 26.7 - - + -
198A PHE* 4.6 2.5 - - + -
203A VAL* 3.6 25.1 - - + -
214A PRO 2.8 18.3 + - - +
215A ALA 3.5 6.7 - - - +
217A ALA* 1.3 74.1 - - - +
219A LEU* 1.3 65.7 + - - +
221A TRP* 3.2 17.0 + - + +
222A HIS* 3.2 24.0 + - + -
258A ILE* 5.5 3.6 - - + -
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 4.2 4.5 - - + -
189A PRO* 4.3 15.0 - - + -
190A LEU* 4.5 11.2 - - + -
215A ALA 2.9 20.1 + - - +
216A GLN* 3.5 5.8 - - - +
218A VAL* 1.3 78.4 - - - +
220A ARG* 1.3 61.2 + - - +
222A HIS* 3.2 7.1 + - - +
223A LEU* 3.1 31.7 + - + +
229A VAL* 4.0 21.5 - - + +
231A PRO* 3.8 23.1 - - + -
242A ASN* 3.5 51.8 - - + +
245A VAL* 4.4 9.0 - - + -
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLN 2.9 17.7 + - - +
217A ALA 3.5 6.1 - - - +
219A LEU* 1.3 75.8 - - - +
221A TRP* 1.3 52.2 + - - +
223A LEU* 3.2 16.5 + - - +
224A GLN* 2.7 75.4 + - - +
245A VAL* 2.9 29.2 + - - +
246A PHE* 3.8 5.9 - - - +
248A PHE* 3.0 44.6 + - + -
249A ASP* 3.9 6.5 - - - +
250A LEU* 3.9 10.1 - - + -
301A SO4 2.6 46.6 + - - -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.0 8.3 - - + -
165A HIS 3.8 7.0 - - - -
166A PRO* 3.7 30.5 - - + -
169A GLN* 3.9 17.7 - - + -
217A ALA 3.1 12.5 + - - +
218A VAL* 3.2 8.9 + - + +
220A ARG* 1.3 73.8 - - - +
222A HIS* 1.3 112.2 + + - +
224A GLN* 3.3 4.0 + - - +
225A LYS* 3.0 55.2 + - + +
250A LEU* 3.9 11.2 - - + +
255A ILE* 3.7 22.6 + - + -
258A ILE* 3.2 39.2 - - + +
259A ASP* 2.7 29.9 + - - -
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Residues in contact with HIS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 2.9 23.8 + - + -
165A HIS* 4.2 0.7 - - - -
186A SER* 3.0 31.7 - - - -
189A PRO* 2.9 37.4 - - + +
218A VAL* 3.2 25.0 + - + -
219A LEU* 3.2 6.6 + - - +
221A TRP* 1.3 100.7 - + - +
223A LEU* 1.3 65.0 + - - +
225A LYS* 3.1 4.5 + - - +
226A GLY 3.1 5.4 + - - -
227A PHE* 2.9 38.2 + + + +
229A VAL* 3.4 21.5 - - + +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLN* 3.0 62.3 + - + +
17A LEU* 4.8 0.4 - - + -
219A LEU* 3.1 27.3 + - + +
220A ARG* 3.4 23.1 - - - +
222A HIS* 1.3 77.1 - - - +
224A GLN* 1.3 54.6 + - - +
226A GLY* 2.7 21.1 + - - -
227A PHE 4.0 1.8 - - - +
229A VAL* 4.1 15.7 - - + -
245A VAL* 3.8 27.4 - - + -
246A PHE* 4.2 15.9 - - + -
301A SO4 5.4 1.3 - - - +
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Residues in contact with GLN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ARG* 2.7 54.3 + - - +
221A TRP 4.0 1.8 - - - +
223A LEU* 1.3 73.2 - - - +
225A LYS* 1.3 60.7 + - - +
226A GLY* 3.0 1.3 + - - -
249A ASP* 3.1 9.0 - - - +
250A LEU* 2.6 41.8 + - - -
252A ASP* 5.2 1.6 + - - -
255A ILE* 2.9 42.3 - - + +
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Residues in contact with LYS 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 5.1 0.7 - - - -
169A GLN* 4.5 8.4 + - - +
221A TRP* 3.0 63.8 + - + +
222A HIS 3.1 5.4 + - - +
224A GLN* 1.3 75.4 - - - +
226A GLY* 1.3 60.0 + - - +
227A PHE* 3.2 45.4 - - + -
255A ILE* 4.7 10.1 - - + -
259A ASP* 3.0 25.4 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il